I'm in agreement with the OP, but I'm pretty dissatisfied as a whole with the entire way that magic and spellcasting works in 3e. However, I found a really good system in EN Publishing's product "Elements of Magic."
It ditches the pre-made spells that have been a staple of D&D in favor of a spell-creation system that can re-create almost all of the core d20 spells, as well as create new custom spells.
It includes a spellpoint system, but there's also a skill-based magic system in EOM: Mythic Earth.
Anyway, I'll stop before I sound any more like an advertisement. But if you don't like the d20 spell system, I highly recommend Elements of Magic.